Variant report

Variant	rs838516
Chromosome Location	chr1:119871207-119871208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10754394	0.93[EUR][1000 genomes]
rs10802089	1.00[EUR][1000 genomes]
rs10923796	0.93[EUR][1000 genomes]
rs1409056	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418024	0.93[EUR][1000 genomes]
rs1418025	0.93[EUR][1000 genomes]
rs1891224	1.00[EUR][1000 genomes]
rs2153738	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2226102	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2243981	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2253988	1.00[EUR][1000 genomes]
rs2254528	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254664	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2257016	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265628	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265630	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2477889	0.82[EUR][1000 genomes]
rs2477890	0.82[EUR][1000 genomes]
rs2885445	0.93[EUR][1000 genomes]
rs6428814	0.93[EUR][1000 genomes]
rs6672571	1.00[EUR][1000 genomes]
rs6694847	1.00[MEX][hapmap]
rs699771	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838512	0.94[ASW][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs838513	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs838514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838515	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838517	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838519	1.00[EUR][1000 genomes]
rs838520	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838523	0.82[EUR][1000 genomes]
rs838524	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838525	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838526	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs838527	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs866788	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs947422	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947423	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947424	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947425	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv547615	chr1:119828542-119875730	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv2761649	chr1:119840645-119925936	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119868000-119871600	Flanking Active TSS	Liver	Liver
2	chr1:119869400-119871800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:119870400-119871800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:119870400-119872000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:119870600-119871400	Weak transcription	Ovary	ovary
6	chr1:119870600-119871600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:119870600-119871600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:119870600-119872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:119870600-119872200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:119870600-119872400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:119870600-119872400	Enhancers	Placenta	Placenta
12	chr1:119870600-119872600	Enhancers	Fetal Stomach	stomach
13	chr1:119870600-119872800	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:119870600-119873000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:119870600-119873200	Weak transcription	Osteobl	bone
16	chr1:119870600-119874400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:119870600-119874600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:119870600-119874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:119870600-119874800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:119870600-119874800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:119870600-119874800	Weak transcription	Esophagus	oesophagus
22	chr1:119870600-119875200	Enhancers	Fetal Muscle Leg	muscle
23	chr1:119870600-119879600	Weak transcription	Fetal Lung	lung
24	chr1:119870600-119879800	Weak transcription	Right Atrium	heart
25	chr1:119870800-119871400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:119870800-119871600	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:119870800-119871600	Enhancers	Fetal Kidney	kidney
28	chr1:119870800-119871800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:119870800-119872000	Enhancers	Colon Smooth Muscle	Colon
30	chr1:119870800-119872200	Weak transcription	Spleen	Spleen
31	chr1:119870800-119872600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:119870800-119872800	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:119870800-119874200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:119870800-119874200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:119870800-119874600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:119870800-119874600	Weak transcription	GM12878-XiMat	blood
37	chr1:119870800-119883400	Weak transcription	Fetal Intestine Small	intestine
38	chr1:119871000-119871400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:119871000-119871600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:119871000-119871800	Enhancers	HepG2	liver
41	chr1:119871000-119872000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:119871000-119872000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:119871000-119872800	Enhancers	H9 Cell Line	embryonic stem cell
44	chr1:119871000-119873000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr1:119871000-119873400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:119871000-119874200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:119871200-119871400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:119871200-119871400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr1:119871200-119872800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:119871200-119874000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links